how do the conditions of the anchorage reflect the conditions inside the ship?

The anchorage was smelly and stagnant, a place perfect for breeding infection. This reflects the conditions inside the ship where an infection of insubordinance and a desire for mutiny were spreading throughout the crew like a disease.

"I don't know about treasure," he said, "but I'll stake my wig there's fever here."

If the conduct of the men had been alarming in the boat, it became truly threatening when they had come aboard. They lay about the deck growling together in talk. The slightest order was received with a black look and grudgingly and carelessly obeyed. Even the honest hands must have caught the infection, for there was not one man aboard to mend another. Mutiny, it was plain, hung over us like a thunder-cloud.